I would encourage you to seek further support in your research community and start fiddling around with RStudio and these various packages. I feel publishing with these types of R packages are more credible in the literature as well. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Many others have stood where you're standing, resulting in a lot of blog posts etc. Although, command line analysis is quite difficult at times to learn and incredibly frustrating, it's not impossible. Therefore, I would advise to use CLC as more of a preliminary analysis tool. This training will be held in the NIH Library Training Room, Building 10, from 9:30 a.m. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). The NIH Library’s Bioinformatics Support Program has organized a CLC Genomics Workbench class for Wednesday, August 31. Hi Cristina, I previously used CLC for RNA-Seq analysis and fiddled with lots of parameters, my final output delivered a low number of differentially expressed genes (DEG) that were uninformative. Message me if you'd like to see some codes I've used or have any other questions. It is essentially a GUI implementation of QIIME2, their algorithms and analysis methods are not 'blackbox' but rather. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Yes, we use CLC Genomics Workbench and their Microbial Genomics Module. Therefore, I would advise to use CLC as more of a preliminary analysis tool. CLC Genomics Workbench Octowebsite maker Comprehensive suite of tools for analysis of next-gen sequencing data including resequencing data, workflow management, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, and trio analysis. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method).
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